The download version of centos6 gives me the same problems. Can I run MRage from the command line if I have a PHIL file that was generated by the GUI? I successfully used phenix.10-2155 GUI to run the toxd tutorial with the MRage package. I retrieved the PHIL file (mr_pipeline_13.eff) used by MRage in the .phenix directory. However, the suggested syntax does not appear to start the program.

The program just sits there and using the top command does not indicate that anything is running.

From: [email protected] <[email protected]> on behalf of Reza Khayat <[email protected]>
Sent: Wednesday, November 23, 2016 9:28 AM
To: Dr. Robert Oeffner; [email protected]
Subject: Re: [phenixbb] Crashing Phenix during MRage

Hi Rob,

I'll give it a try.

Best wishes,
Reza

Reza Khayat, PhD

Assistant Professor

City College of New York

Department of Chemistry

New York, NY 10031

From: Dr. Robert Oeffner <[email protected]>
Sent: Wednesday, November 23, 2016 9:24 AM
To: Reza Khayat; [email protected]
Subject: Re: [phenixbb] Crashing Phenix during MRage

Dear professor Reza,

Sorry for the problems you’re having with MRage. If it wasn’t for the issues you’re having installing the latest official phenix release I was gonna suggest you try running MRage with that. Much has changed in the underlying code. Have you tried the centos6 installer version instead?

Regards,

Rob

--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html

From: Reza Khayat

Sent: Wednesday, November 23, 2016 2:05 PM

To: [email protected]

Subject: [phenixbb] Crashing Phenix during MRage

Hi,

MRage stops running after sometime with the following error:

===========================================

Process Process-1:29434:
Traceback (most recent call last):
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError
Process Process-1:29436:
Traceback (most recent call last):
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError
Process Process-1:29438:
Traceback (most recent call last):
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError
Process Process-1:29440:
Traceback (most recent call last):
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError

** (gedit:5901): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-pJCFNfwEtI: Connection refused

(gedit:5901): GLib-GIO-ERROR **: No GSettings schemas are installed on the system

==============================================================================